Hi all-

The MODELLER documentation at https://salilab.org/modeller/manual/node149.html#MEMB:iodata.convertmodres says the following:

"Some special handling is done for certain commonly-used modified residues. The MSE residue type is mapped to the regular MET amino acid, and the SE atom in this residue is mapped to SD. The MEX and ABU residue types are both mapped to CYS."

According to https://salilab.org/archives/modeller_usage/2003/msg00051.html the reason for this is that MEX is "cysteine bridged with beta-mercaptoethanol".

I recently encountered PDB ID 3OW6. This structure includes a ligand labeled MEX. The ligand does not resemble CYS, and the presence of MEX causes an error. I'm reluctant to set io_data.convert_modres to False, because I'd like to handle other modified residues (ex. MSE).

I was able to work around the issue, so it didn't impact me too much. But I thought I should say something in case others run into the same issue. I see that the ligand CME does resemble CYS, with beta-mercaptoethanol attached through a disulfide bond. Is it possible that MEX and CME are switched?

Best,

Daniel Evans